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E-raamat: Introduction to Genomic Signal Processing with Control

(Texas A&M University, College Station, USA), (Texas A&M University, College Station, USA)
  • Formaat: 288 pages
  • Ilmumisaeg: 08-Oct-2018
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781420006674
  • Formaat - PDF+DRM
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  • Formaat: 288 pages
  • Ilmumisaeg: 08-Oct-2018
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781420006674

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Studying large sets of genes and their collective function requires tools that can easily handle huge amounts of information. Recent research indicates that engineering approaches for prediction, signal processing, and control are well suited for studying multivariate interactions. A tutorial guide to the current engineering research in genomics, Introduction to Genomic Signal Processing with Control provides a state-of-the-art account of the use of control theory to obtain intervention strategies for gene regulatory networks.

The book builds up the necessary molecular biology background with a basic review of organic chemistry and an introduction of DNA, RNA, and proteins, followed by a description of the processes of transcription and translation and the genetic code that is used to carry out the latter. It discusses control of gene expression, introduces genetic engineering tools such as microarrays and PCR, and covers cell cycle control and tissue renewal in multi-cellular organisms.

The authors then delineate how the engineering approaches of classification and clustering are appropriate for carrying out gene-based disease classification. This leads naturally to expression prediction, which in turn leads to genetic regulatory networks. The book concludes with a discussion of control approaches that can be used to alter the behavior of such networks in the hope that this alteration will move the network from a diseased state to a disease-free state.

Written by recognized leaders in this emerging field, the book provides the exact amount of molecular biology required to understand the engineering applications. It is a self-contained resource that spans the diverse disciplines of molecular biology and electrical engineering.
1 Introduction
1(4)
2 Review of Organic Chemistry
5(22)
2.1 Electrovalent and Covalent Bonds
6(3)
2.2 Some Chemical Bonds and Groups Commonly Encountered in Biological Molecules
9(4)
2.3 Building Blocks for Common Organic Molecules
13(14)
2.3.1 Sugars
13(4)
2.3.2 Fatty Acids
17(1)
2.3.3 Amino Acids
18(2)
2.3.4 Nucleotides
20(7)
3 Energy Considerations in Biochemical Reactions
27(10)
3.1 Some Common Biochemical Reactions
28(2)
3.1.1 Photosynthesis
28(1)
3.1.2 Cellular Respiration
29(1)
3.1.3 Oxidation and Reduction
29(1)
3.2 Role of Enzymes
30(2)
3.3 Feasibility of Chemical Reactions
32(2)
3.4 Activated Carrier Molecules and Their Role in Biosynthesis
34(3)
4 Proteins
37(16)
4.1 Protein Structure and Function
37(4)
4.1.1 The a-helix and the 0-sheet
38(3)
4.2 Levels of Organization in Proteins
41(2)
4.3 Protein Ligand Interactions
43(2)
4.4 Isolating Proteins from Cells
45(1)
4.5 Separating a Mixture of Proteins
46(2)
4.5.1 Column Chromatography
47(1)
4.5.2 Gel Electrophoresis
47(1)
4.6 Protein Structure Determination
48(1)
4.7 Proteins That Are Enzymes
49(4)
5 DNA
53(10)
6 Transcription and Translation
63(14)
6.1 Transcription
64(5)
6.2 Translation
69(8)
7 Chromosomes and Gene Regulation
77(12)
7.1 Organization of DNA into Chromosomes
78(4)
7.2 Gene Regulation
82(7)
8 Genetic Variation
89(12)
8.1 Genetic Variation in Bacteria
89(5)
8.1.1 Bacterial Mating
90(2)
8.1.2 Gene Transfer by Bacteriophages
92(1)
8.1.3 Transposons
93(1)
8.2 Sources of Genetic Change in Eucaryotic Genomes
94(7)
8.2.1 Gene Duplication
94(2)
8.2.2 Transposable Elements and Viruses
96(2)
8.2.3 Sexual Reproduction and the Reassortment of Genes
98(3)
9 DNA Technology
101(16)
9.1 Techniques for Analyzing DNA Molecules
101(4)
9.2 Nucleic Acid Hybridization and Associated Techniques
105(2)
9.3 Construction of Human Genomic and cDNA Libraries
107(2)
9.4 Polymerase Chain Reaction (PCR)
109(3)
9.5 Genetic Engineering
112(7)
9.5.1 Engineering DNA Molecules, Proteins and RNAs
112(1)
9.5.2 Engineering Mutant Haploid Organisms
112(2)
9.5.3 Engineering Transgenic Animals
114(3)
10 Cell Division 117(10)
10.1 Mitosis and Cytokinesis
119(4)
10.2 Meiosis
123(4)
11 Cell Cycle Control, Cell Death and Cancer 127(10)
11.1 Cyclin-Dependent Kinases and Their Role
128(3)
11.2 Control of Cell Numbers in Multicellular Organisms
131(1)
11.3 Programmed Cell Death
132(1)
11.4 Cancer as the Breakdown of Cell Cycle Control
133(4)
12 Expression Microarrays 137(10)
12.1 cDNA Microarrays
138(7)
12.1.1 Normalization
140(2)
12.1.2 Ratio Analysis
142(3)
12.2 Synthetic Oligonucleotide Arrays
145(2)
13 Classification 147(20)
13.1 Classifier Design
147(11)
13.1.1 Bayes Classifier
148(1)
13.1.2 Classification Rules
148(3)
13.1.3 Constrained Classifier Design
151(3)
13.1.4 Regularization for Quadratic Discriminant Analysis
154(3)
13.1.5 Regularization by Noise Injection
157(1)
13.2 Feature Selection
158(3)
13.3 Error Estimation
161(7)
13.3.1 Error Estimation Using the Training Data
162(1)
13.3.2 Performance Issues
163(4)
14 Clustering 167(14)
14.1 Examples of Clustering Algorithms
168(5)
14.1.1 k-means
168(1)
14.1.2 Fuzzy k-means
169(1)
14.1.3 Self-Organizing Maps
170(1)
14.1.4 Hierarchical Clustering
171(2)
14.2 Clustering Accuracy
173(3)
14.2.1 Model-Based Clustering Error
173(1)
14.2.2 Application to Real Data
174(2)
14.3 Cluster Validation
176(5)
15 Genetic Regulatory Networks 181(16)
15.1 Nonlinear Dynamical Modeling of Gene Networks
182(2)
15.2 Boolean Networks
184(4)
15.2.1 Boolean Model
184(3)
15.2.2 Coefficient of Determination
187(1)
15.3 Probabilistic Boolean Networks
188(4)
15.4 Network Inference
192(5)
16 Intervention 197(10)
16.1 PBN Notation
198(1)
16.2 Intervention by Flipping the Status of a Single Gene
199(4)
16.3 Intervention to Alter the Steady-State Behavior
203(4)
17 External Intervention Based on Optimal Control Theory 207(46)
17.1 Finite-Horizon-Control
208(12)
17.1.1 Solution Using Dynamic Programming
211(1)
17.1.2 A Simple Illustrative Example
212(3)
17.1.3 Melanoma Example
215(5)
17.2 External Intervention in the Imperfect Information Case
220(6)
17.2.1 Melanoma Example
221(5)
17.3 External Intervention in the Context-Sensitive Case
226(6)
17.3.1 Melanoma Example
229(3)
17.4 External Intervention for a Family of Boolean Networks
232(6)
17.4.1 Melanoma Example
235(3)
17.5 External Intervention in the Infinite Horizon Case
238(10)
17.5.1 Optimal Control Solution
240(4)
17.5.2 Melanoma Example
244(4)
17.6 Concluding Remarks
248(5)
References 253(12)
Index 265


Aniruddha Datta, Edward R. Dougherty